This article reviews the relationships between government and church health providers within sub-Saharan Africa with a particular focus on East and Southern Africa. This is of particular interest at this time, given the changing configuration of the health sector in many countries as a result of health sector reform policies. The article provides a historical overview of the development and emerging role of the church health services within this changing environment. The factors affecting the relationship between the government and church sector are identified. These include differences in objectives, types of service provided, and the organizational culture and management styles. The paper then explores key issues seen to affect the future pattern of relationships including the changing scene, and identifies different models for relationships and implications for key actors including the Ministry of Health, church health agencies and coordinating bodies. The article concludes that church health services will continue to play a key role in health care in sub-Saharan Africa; however, there are challenges facing them and both parties need to develop a response to these.